The Pentagon created the Office of Detainee Affairs, and with it Stimson's post, in July 2004:[4][5]

An as-yet-unnamed deputy assistant secretary who will report to the undersecretary for policy will head the office. The new deputy will chair a joint committee composed of the undersecretary for intelligence and representatives from the Joint Staff, the Office of General Counsel, the Department of the Army, and others who might be involved in detainee affairs.

Stimson, an attorney by profession, was formerly a U.S. Navy JAG officer from 1992-1997.[6]

Stimson first received press attention in October 2006, when he told Reuters that more than 300 Guantánamo detainees might remain there for the rest of their lives because nations refused to accept them.[7]

In January 2007, he made comments concerning the legal representation of Guantánamo detainees stating that "corporate CEOs seeing this should ask firms to choose between lucrative retainers and representing terrorists."[8] The Pentagon later issued a statement that Stimson's comments were not representative of Pentagon policy.[9][10]

On January 17, 2007, Stimson wrote a letter of apology, published in the Washington Post.[11][12][13] His apology was criticized by the New York Times in an editorial, for the appearance of insincerity.[14] In 2017, Stimson said his comments made one decade ago were a mistake that do not represent his professional views: "I made a boneheaded statement, quite frankly it was an emotional response generated by my loss of my 295 colleagues who...were killed on 9/11 at the World Trade Center."[15]